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- EMDB-6499: Structural insights into the regulatory mechanism of ATM kinase a... -

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Basic information

Entry
Database: EMDB / ID: EMD-6499
TitleStructural insights into the regulatory mechanism of ATM kinase activation
Map dataReconstruction of monomeric ATM kinase
Sample
  • Sample: Monomeric ATM kinase
  • Protein or peptide: Monomeric ATM kinase
KeywordsDNA-damage response / ataxia telangiectasia / PIKK
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 28.0 Å
AuthorsLau WCY / Li Y / Liu Z / Gao Y / Zhang Q / Huen MSY
CitationJournal: Cell Cycle / Year: 2016
Title: Structure of the human dimeric ATM kinase.
Authors: Wilson C Y Lau / Yinyin Li / Zhe Liu / Yuanzhu Gao / Qinfen Zhang / Michael S Y Huen /
Abstract: DNA-double strand breaks activate the serine/threonine protein kinase ataxia-telangiectasia mutated (ATM) to initiate DNA damage signal transduction. This activation process involves ...DNA-double strand breaks activate the serine/threonine protein kinase ataxia-telangiectasia mutated (ATM) to initiate DNA damage signal transduction. This activation process involves autophosphorylation and dissociation of inert ATM dimers into monomers that are catalytically active. Using single-particle electron microscopy (EM), we determined the structure of dimeric ATM in its resting state. The EM map could accommodate the crystal structure of the N-terminal truncated mammalian target of rapamycin (mTOR), a closely related enzyme of the phosphatidylinositol 3-kinase-related protein kinase (PIKK) family, allowing for the localization of the N- and the C-terminal regions of ATM. In the dimeric structure, the actives sites are buried, restricting the access of the substrates to these sites. The unanticipated domain organization of ATM provides a basis for understanding its mechanism of inhibition.
History
DepositionNov 2, 2015-
Header (metadata) releaseDec 9, 2015-
Map releaseNov 16, 2016-
UpdateNov 16, 2016-
Current statusNov 16, 2016Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.45
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6499.gif

Downloads & links

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Map

FileDownload / File: emd_6499.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of monomeric ATM kinase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.61 Å/pix.
x 100 pix.
= 461. Å		4.61 Å/pix.
x 100 pix.
= 461. Å		4.61 Å/pix.
x 100 pix.
= 461. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.61 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45 / Movie #1: 0.45
Minimum - Maximum-0.0814552 - 1.07092738
Average (Standard dev.)0.00547454 (±0.05157611)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 461.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.614.614.61
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z461.000461.000461.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-0.0811.0710.005

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Supplemental data

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Sample components

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Entire : Monomeric ATM kinase

EntireName: Monomeric ATM kinase
Components
  • Sample: Monomeric ATM kinase
  • Protein or peptide: Monomeric ATM kinase

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Supramolecule #1000: Monomeric ATM kinase

SupramoleculeName: Monomeric ATM kinase / type: sample / ID: 1000 / Details: The sample was mono disperse / Oligomeric state: Monomer / Number unique components: 1
Molecular weightTheoretical: 350 KDa

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Macromolecule #1: Monomeric ATM kinase

MacromoleculeName: Monomeric ATM kinase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 350 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293T / Recombinant plasmid: pcDNA-FLAG-His-ATM wt

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.02 mg/mL
BufferpH: 8 / Details: 25 mM Tris, 100 mM NaCl, 1 mM TCEP, 10% glycerol
StainingType: NEGATIVE / Details: 1% w/v uranyl acetate
GridDetails: Continuous carbon coated copper grids
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 2010
TemperatureAverage: 296 K
DateJul 1, 2015
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 251 / Average electron dose: 25 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: class average
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: OTHER / Software - Name: PRIME, EMAN2 / Number images used: 6546

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Atomic model buiding 1

Initial modelPDB ID:

4jsv


Chain - Chain ID: A
SoftwareName: Chimera
DetailsResidues 2021-2118 are removed
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: cross correlation coefficient

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